COMBINATORIAL CHEMISTRY - definition - Combinatorial chemistry can be defined as the
synthesis of different chemical compounds as ensembles ('libraries') and the
immediate (maybe 'in-situ') screening of them for desirable properties. Combinational chemistry is potentially an
efficient route to new drugs, catalysts, and other compounds and new materials.

Protein
Synthesis

Two theoretical combinations
of two different alpha amino acids, differing only in the R and R' groups to form a
dipeptide.

H2N-CHR-COOH
+ H2N-CHR'-COOH

{H2N-CHR-CO-NH-CHR'-COOH
or H2N-CHR'-CONH-CHR-COOH} + H2O

Note:

This is a
condensation reaction, because a small molecule (water) is
eliminated as the two molecules join to form a bigger molecule,
a 'natural condensation polymer' and hence the name 'polypeptide' for
a protein structure.

-NH-CO-
is the secondary amide 'peptide linkage' and the reaction
is illustrated below with aminoethanoic acid, (glycine)
and 2-aminopropanoic acid (alanine) showing the
two possible di-peptide products (GlyAla or AlaGly).

In this case, both dipeptides
have one chiral carbon, >CH-CH3 and >CH-NH2
respectively.

Since each
of the two possibilities is stereochemically different, not
surprisingly, you would expect a different enzyme (with
cofactor?) for each alternative.

orH2O

In abbreviated
structural formula style, the reaction in terms of possible zwitterions
would be ...

A more complex situation
is tabulated below, showing the nine possible dipeptides that can
theoretically be formed from just from
three different amino acids. The possibilities are greatly expanded if the
permutations of tripeptides etc. were to be considered, and this ignores
chiral isomers!

Possible amino acids
X and Y, and possible XY di-peptides formed

Y = A1

Y = A2

Y = A3

X = A1

A1A1

A1A2

A1A3

X = A2

A2A1

A2A2

A2A3

X = A3

A3A1

A3A2

A3A3

These days it is possible
to 'automatically' synthesise polypeptides in a 'peptide synthesiser'
into which, the required reactants are fed in a pre-programmed way, so all
sorts of permutations can be prepared. The polypeptides can be prepared or
'grown' on polystyrene beads - an example of solid phase chemistry. This
has positive 'efficiency' implications for the pharmaceutical industry
e.g. some
polypeptides are used as drugs and their structure is effectively a
'mini-protein'. It is possible to synthesise a huge variety of
permutations using this combinational chemistry, analyse them to validate their structure and then test them for
their biological/pharmacological activity. This idea can be used for a variety
of organic synthesis, not just for amino acids => polypeptide, and this,
since the 1990's is speeding up the development of drugs and other
biologically active molecules.

The complete
hydrolysis into the
constituent alpha-amino acids can be achieved by heating the protein with
5-6M hydrochloric acid in a sealed tube at 100-120oC, for
10-24 hours. A partial and selective/specific hydrolysis into
short peptide sequences can be done under much milder conditions using
enzymes such as the protease trypsin, found in the small intestine.
There are other much more elaborate methods involving chemical
modification of the terminal amino acid residue, to obtain specific
amino acid residue sequencing, but these are well beyond the scope of
this web page (i.e. UK GCE courses). The resulting
hydrolysis mixture can be analysed by e.g.

(i) paper/thin
layer chromatography, often in two dimensions using two different
solvents (paper rotated 90o between solvents). The colourless
amino acids can be made visible by spraying the chromatography
paper/plates with ninhydrin reagent. Purple spots show up
from the coloured compound formed from the combination of the amino acid
with ninhydrin.

(ii)
electrophoresis, in which the ionic forms of the amino acids are
separated by movement in a buffered aqueous gel medium under the
influence of an applied electric field (from d.c. voltage electrodes).
The different amino acid mobilities depend on the average total +ve or
-ve charge in a particular buffer. The amino acids form bands which can
be detected-analysed by using staining techniques or uv
light fluorescence. The technique can also be applied to the analysis
of protein or nucleic acid mixtures, and the latter can be
detected using a radioactive phosphorus tracer 32P (in
the laboratory you should only deal with stable 31P).

In all cases the
techniques can be calibrated using pure samples of known amino acids,
proteins or nucleic acids etc.

More on Combinatorial Chemistry

Combinational chemistry:

Combinatorial chemistry
is a means of automatically synthesising a range of different chemical compounds
from ensembles called 'libraries' and the efficient screening of the
different molecular 'combinations' for desirable properties which
maybe materials with physically desirable properties or drugs with
particular advantageous pharmacological properties.

The laboratory synthesis of polypeptides
has already been described above and the same principles can
also be applied to the synthesis of drugs.

The 'active' or 'interacting'
part of a
molecule is called pharmacophore
group and changing its nature and the associated 'molecular
architecture' around it, may improve or change its pharmacological
activity.

A pharmacophore is a group of atoms which confers pharmacological
activity on a molecule.

It is possible to rapidly, and automatically, synthesise lots
of variations from selected to reactants and then screen the products
for their pharmacological activity.